Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiles of the aerenchy maformation in maize using laser microdissection

ABSTRACT: To adapt to waterlogging in soil, some gramineous plants, such as maize (Zea mays), form lysigenous aerenchyma in the root cortex. Ethylene, which is accumulated during waterlogging, promotes aerenchyma formation. Aerencyma is formedonly in cortex in maise root. Therevore, aerenchyma is one of the model of programmed cell death. However, the molecular mechanism of aerenchyma formation is not understood. Therefore we isolated only cortex cells in maize primary root using laser microdissection. And microarray analysis was perforemed to identify the arechyma formation related genes. For microarray analysis, we designed 4 different experiments. Basal part and apical part of root were used for 1st experiment because arenchyma was formed in basal part of root, but not in apex. In second experiment, basal part of root with 6 hours waterlogged treatment and without treatment were used. And, as aerenchyma was induced by ethylene, ethylene and 1-MCP (inhibitor of ethylen perception) were used for experiment3 and 4. Gene expression analysis in 4 kinds of samples (cortex in basal reagion of maize primary root which were treated with waterlogged condition, aerobic condition, ethylene and 1-MCP and cortex in apical reagion of maize primary root which were treated with waterlogged conditio)

ORGANISM(S): Zea mays

SUBMITTER: Hirokazu Takahashi

PROVIDER: E-GEOD-26897 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:All above ground organs of higher plants are ultimately derived from specialized organogenic structures termed shoot apical meristems (SAMs). The SAM exhibits distinctive structural organization, marked by cell layering. Maize SAMs are comprised of two cell layers, L1 (single cell layered tunica) and L2 (corpus). To identify genes required for layer-specific functions intact maize SAMs were fixed, embedded in paraffin and sectioned. L1 and L2 cells were isolated from these sections via laser capture microdissection (LCM). RNA was isolated from six biological replications of L1 and L2, amplified and hybridized to microarrays spotted with ~37,000 maize cDNA clones. This experiment identified ~700 ESTs that are preferentially expressed in the L1 or the L2 (P <0.001). The L1-up-regulated ESTs included ZmOCL1 and ZmOCL4, which are known to exhibit L1-specific expression in the maize SAM. The L2-up-regulated ESTs included KNOTTED1, whose transcripts are known to accumulate in the L2 but not in the L1 of the maize SAM. Differentially expressed ESTs included genes involved in transcription, signal transduction, transport and metabolism, many of which are novel candidates that are required for layer-specific functions in the maize SAM. Several L1-up-regulated ESTs were annotated as yabby family genes or basic helix-loop-helix transcription factor-like genes, which have not previously been reported as having layer-specific expression in the SAM. Novel WW domain-containing genes (WW genes) were identified in this study. The WW domain mediates protein-protein interactions, often with signal transduction components. These WW genes were substantially up-regulated in the L1 relative to the L2. Keywords: Cell Type Comparison An experimental aim is to identify genes that are differentially expressed in distinct histological cell layers of maize SAM by comparing the transcript accumulation between L1 (single cell layered tunica) and L2 (corpus) using cDNA microarrays that have over 37,000 informative spots from maize.

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Gene expression profiles of the aerenchy maformation in maize using laser microdissection

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